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Alessandro Senes, Ph.D. - Publications

2001 Yale University, New Haven, CT 
 2008- Biochemistry University of Wisconsin, Madison, Madison, WI 
Structural biology

28 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Anderson SM, Mueller BK, Lange E, Senes A. A combination of Cα-H hydrogen bonds and van der Waals packing modulates the stability of GxxxG-mediated dimers in membranes. Journal of the American Chemical Society. PMID 29028318 DOI: 10.1021/jacs.7b07505  0.6
2015 Zhang Z, Subramaniam S, Kale J, Liao C, Huang B, Brahmbhatt H, Condon SG, Lapolla SM, Hays FA, Ding J, He F, Zhang XC, Li J, Senes A, Andrews DW, et al. BH3-in-groove dimerization initiates and helix 9 dimerization expands Bax pore assembly in membranes. The Embo Journal. PMID 26702098 DOI: 10.15252/embj.201591552  0.96
2015 Ma G, Wei M, He L, Liu C, Wu B, Zhang SL, Jing J, Liang X, Senes A, Tan P, Li S, Sun A, Bi Y, Zhong L, Si H, et al. Inside-out Ca(2+) signalling prompted by STIM1 conformational switch. Nature Communications. 6: 7826. PMID 26184105 DOI: 10.1038/ncomms8826  0.96
2014 Khadria AS, Mueller BK, Stefely JA, Tan CH, Pagliarini DJ, Senes A. A Gly-zipper motif mediates homodimerization of the transmembrane domain of the mitochondrial kinase ADCK3. Journal of the American Chemical Society. 136: 14068-77. PMID 25216398 DOI: 10.1021/ja505017f  0.96
2014 Subramaniam S, Senes A. Backbone dependency further improves side chain prediction efficiency in the Energy-based Conformer Library (bEBL). Proteins. 82: 3177-87. PMID 25212195 DOI: 10.1002/prot.24685  0.96
2014 Gromek KA, Suchy FP, Meddaugh HR, Wrobel RL, LaPointe LM, Chu UB, Primm JG, Ruoho AE, Senes A, Fox BG. The oligomeric states of the purified sigma-1 receptor are stabilized by ligands Journal of Biological Chemistry. 289: 20333-20344. PMID 24847081 DOI: 10.1074/jbc.M113.537993  0.96
2014 Mueller BK, Subramaniam S, Senes A. A frequent, GxxxG-mediated, transmembrane association motif is optimized for the formation of interhelical Cα-H hydrogen bonds. Proceedings of the National Academy of Sciences of the United States of America. 111: E888-95. PMID 24569864 DOI: 10.1073/pnas.1319944111  0.96
2013 Khadria AS, Senes A. The transmembrane domains of the bacterial cell division proteins FtsB and ftsl form a stable high-order oligomer Biochemistry. 52: 7542-7550. PMID 24083359 DOI: 10.1021/bi4009837  0.96
2013 LaPointe LM, Taylor KC, Subramaniam S, Khadria A, Rayment I, Senes A. Structural organization of FtsB, a transmembrane protein of the bacterial divisome. Biochemistry. 52: 2574-85. PMID 23520975 DOI: 10.1021/bi400222r  0.96
2013 Khadria A, Senes A. Measurement of transmembrane peptide interactions in liposomes using förster resonance energy transfer (FRET) Methods in Molecular Biology. 1063: 19-36. DOI: 10.1007/978-1-62703-583-5_2  0.96
2013 Ghirlanda G, Senes A. Preface Methods in Molecular Biology. 1063: V-VI.  0.96
2012 Subramaniam S, Senes A. An energy-based conformer library for side chain optimization: improved prediction and adjustable sampling. Proteins. 80: 2218-34. PMID 22576292 DOI: 10.1002/prot.24111  0.96
2012 Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G, Senes A. Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL). Journal of Computational Chemistry. 33: 1645-61. PMID 22565567 DOI: 10.1002/jcc.22968  0.96
2011 Hsin J, LaPointe LM, Kazy A, Chipot C, Senes A, Schulten K. Oligomerization state of photosynthetic core complexes is correlated with the dimerization affinity of a transmembrane helix. Journal of the American Chemical Society. 133: 14071-81. PMID 21790140 DOI: 10.1021/ja204869h  0.96
2011 Senes A. Computational design of membrane proteins. Current Opinion in Structural Biology. 21: 460-6. PMID 21763125 DOI: 10.1016/  0.96
2011 Subramaniam S, Natarajan S, Senes A. A machine learning based approach to improve sidechain optimization 2011 Acm Conference On Bioinformatics, Computational Biology and Biomedicine, Bcb 2011. 478-480. DOI: 10.1145/2147805.2147875  0.96
2010 Korendovych IV, Senes A, Kim YH, Lear JD, Fry HC, Therien MJ, Blasie JK, Walker FA, Degrado WF. De novo design and molecular assembly of a transmembrane diporphyrin-binding protein complex. Journal of the American Chemical Society. 132: 15516-8. PMID 20945900 DOI: 10.1021/ja107487b  0.96
2010 Berger BW, Kulp DW, Span LM, DeGrado JL, Billings PC, Senes A, Bennett JS, DeGrado WF. Consensus motif for integrin transmembrane helix association. Proceedings of the National Academy of Sciences of the United States of America. 107: 703-8. PMID 20080739 DOI: 10.1073/pnas.0910873107  0.96
2008 McAllister KA, Zou H, Cochran FV, Bender GM, Senes A, Fry HC, Nanda V, Keenan PA, Lear JD, Saven JG, Therien MJ, Blasie JK, DeGrado WF. Using alpha-helical coiled-coils to design nanostructured metalloporphyrin arrays. Journal of the American Chemical Society. 130: 11921-7. PMID 18710226 DOI: 10.1021/ja800697g  0.96
2007 Finikova OS, Troxler T, Senes A, DeGrado WF, Hochstrasser RM, Vinogradov SA. Energy and electron transfer in enhanced two-photon-absorbing systems with triplet cores. The Journal of Physical Chemistry. A. 111: 6977-90. PMID 17608457 DOI: 10.1021/jp071586f  0.96
2007 Senes A, Chadi DC, Law PB, Walters RF, Nanda V, Degrado WF. E(z), a depth-dependent potential for assessing the energies of insertion of amino acid side-chains into membranes: derivation and applications to determining the orientation of transmembrane and interfacial helices. Journal of Molecular Biology. 366: 436-48. PMID 17174324 DOI: 10.1016/j.jmb.2006.09.020  0.96
2006 Fang C, Senes A, Cristian L, DeGrado WF, Hochstrasser RM. Amide vibrations are delocalized across the hydrophobic interface of a transmembrane helix dimer. Proceedings of the National Academy of Sciences of the United States of America. 103: 16740-5. PMID 17075037 DOI: 10.1073/pnas.0608243103  0.96
2004 Lehnert U, Xia Y, Royce TE, Goh CS, Liu Y, Senes A, Yu H, Zhang ZL, Engelman DM, Gerstein M. Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions. Quarterly Reviews of Biophysics. 37: 121-46. PMID 15999419 DOI: 10.1017/S003358350400397X  0.96
2004 Senes A, Engel DE, DeGrado WF. Folding of helical membrane proteins: the role of polar, GxxxG-like and proline motifs. Current Opinion in Structural Biology. 14: 465-79. PMID 15313242 DOI: 10.1016/  0.96
2003 Engelman DM, Chen Y, Chin CN, Curran AR, Dixon AM, Dupuy AD, Lee AS, Lehnert U, Matthews EE, Reshetnyak YK, Senes A, Popot JL. Membrane protein folding: beyond the two stage model. Febs Letters. 555: 122-5. PMID 14630331 DOI: 10.1016/S0014-5793(03)01106-2  0.96
2002 Lin J, Qian J, Greenbaum D, Bertone P, Das R, Echols N, Senes A, Stenger B, Gerstein M. GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing. Nucleic Acids Research. 30: 4574-82. PMID 12384605  0.96
2001 Senes A, Ubarretxena-Belandia I, Engelman DM. The Calpha ---H...O hydrogen bond: a determinant of stability and specificity in transmembrane helix interactions. Proceedings of the National Academy of Sciences of the United States of America. 98: 9056-61. PMID 11481472 DOI: 10.1073/pnas.161280798  0.96
2000 Senes A, Gerstein M, Engelman DM. Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions. Journal of Molecular Biology. 296: 921-36. PMID 10677292 DOI: 10.1006/jmbi.1999.3488  0.96
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